Meta-analysis

The response to antigen, virus, or mRNA vaccine uptake was compared across samples, the general approach:

  • Differentially expressed genes were identified for Ag-high vs -low (or virus, mRNA vaccine, etc.) LECs for each sample. LECs were not divided into subsets.
  • PCA was performed using the fold change in expression for DEGs (Ag-high / Ag-low), the top genes from PC1 were identified
  • A random effects model was used to identify genes that show the most consistent response across samples.
  1. PCA plot showing similarity of the Ag/virus/vaccine response across samples
  2. The top genes from PC1 were clustered based on fold change in expression
  3. Gene ontology terms are shown for each gene cluster from B.
  4. The top genes with the most consistent response across samples were clustered as in B.
  5. Gene ontology terms are shown for each gene cluster from D.



Endocytic receptors

Project 3 will use LYTACs and EndoTags to direct antigen into specific endocytic compartments. Expression of relevant receptors is shown below.

M6pr



Sort1



Tfrc



Igf2r



Session info

## R version 4.3.1 (2023-06-16)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 22.04.5 LTS
## 
## Matrix products: default
## BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so;  LAPACK version 3.10.0
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8          LC_NUMERIC=C                 
##  [3] LC_TIME=en_US.UTF-8           LC_COLLATE=en_US.UTF-8       
##  [5] LC_MONETARY=en_US.UTF-8       LC_MESSAGES=en_US.UTF-8      
##  [7] LC_PAPER=en_US.UTF-8          LC_NAME=en_US.UTF-8          
##  [9] LC_ADDRESS=en_US.UTF-8        LC_TELEPHONE=en_US.UTF-8     
## [11] LC_MEASUREMENT=en_US.UTF-8    LC_IDENTIFICATION=en_US.UTF-8
## 
## time zone: America/Denver
## tzcode source: system (glibc)
## 
## attached base packages:
##  [1] tools     stats4    grid      stats     graphics  grDevices utils    
##  [8] datasets  methods   base     
## 
## other attached packages:
##  [1] sp_2.1-0                  sf_1.0-16                
##  [3] SpatialOmicsOverlay_1.0.0 umap_0.2.10.0            
##  [5] GeoMxWorkflows_1.6.0      GeomxTools_3.4.0         
##  [7] NanoStringNCTools_1.8.0   cli_3.6.1                
##  [9] devtools_2.4.5            usethis_2.2.2            
## [11] here_1.0.1                broom_1.0.5              
## [13] knitr_1.44                lubridate_1.9.3          
## [15] forcats_1.0.0             stringr_1.5.0            
## [17] dplyr_1.1.3               purrr_1.0.2              
## [19] readr_2.1.4               tidyr_1.3.0              
## [21] tibble_3.2.1              tidyverse_2.0.0          
## [23] pzfx_0.3.0                png_0.1-8                
## [25] xlsx_0.6.5                openxlsx_4.2.5.2         
## [27] qs_0.25.5                 ggtree_3.8.2             
## [29] MetBrewer_0.2.0           ggVennDiagram_1.5.2      
## [31] ggtrace_0.2.0.9000        ggtext_0.1.2             
## [33] patchwork_1.2.0           colorblindr_0.1.0        
## [35] colorspace_2.1-0          RColorBrewer_1.1-3       
## [37] ggrepel_0.9.3             cowplot_1.1.1            
## [39] ggbeeswarm_0.7.2          ggforce_0.4.1            
## [41] scales_1.3.0              ggspruce_0.1.0           
## [43] caret_6.0-94              lattice_0.21-8           
## [45] ggplot2_3.5.1             furrr_0.3.1              
## [47] future_1.33.0             ranger_0.15.1            
## [49] rsample_1.2.0             gtools_3.9.4             
## [51] boot_1.3-28.1             mixtools_2.0.0           
## [53] GOSemSim_2.26.1           org.Mm.eg.db_3.17.0      
## [55] AnnotationDbi_1.62.2      IRanges_2.34.1           
## [57] S4Vectors_0.38.2          Biobase_2.60.0           
## [59] BiocGenerics_0.46.0       msigdbr_7.5.1            
## [61] enrichplot_1.20.3         clusterProfiler_4.8.3    
## [63] biomaRt_2.56.1            gprofiler2_0.2.2         
## [65] hdf5r_1.3.11              M3Drop_1.26.0            
## [67] numDeriv_2016.8-1.1       djvdj_0.1.0              
## [69] harmony_1.1.0             presto_1.0.0             
## [71] data.table_1.14.8         Rcpp_1.0.11              
## [73] clustifyrdata_1.1.0       clustifyr_1.12.0         
## [75] SeuratObject_4.1.4        Seurat_4.4.0             
## [77] ComplexHeatmap_2.16.0     meta_8.0-1               
## [79] metadat_1.2-0            
## 
## loaded via a namespace (and not attached):
##   [1] igraph_1.5.1                ica_1.0-3                  
##   [3] plotly_4.10.2               Formula_1.2-5              
##   [5] zlibbioc_1.46.0             tidyselect_1.2.0           
##   [7] bit_4.0.5                   doParallel_1.0.17          
##   [9] clue_0.3-65                 rjson_0.2.21               
##  [11] urlchecker_1.0.1            blob_1.2.4                 
##  [13] S4Arrays_1.0.6              parallel_4.3.1             
##  [15] plotrix_3.8-4               ggplotify_0.1.2            
##  [17] outliers_0.15               askpass_1.2.0              
##  [19] openssl_2.1.1               goftest_1.2-3              
##  [21] GenSA_1.1.14                kernlab_0.9-32             
##  [23] densEstBayes_1.0-2.2        uwot_0.1.16                
##  [25] shadowtext_0.1.2            curl_5.1.0                 
##  [27] mime_0.12                   evaluate_0.22              
##  [29] tidytree_0.4.5              tiff_0.1-12                
##  [31] leiden_0.4.3                stringi_1.7.12             
##  [33] pROC_1.18.5                 backports_1.4.1            
##  [35] lmerTest_3.1-3              XML_3.99-0.14              
##  [37] httpuv_1.6.11               magrittr_2.0.3             
##  [39] rappdirs_0.3.3              splines_4.3.1              
##  [41] prodlim_2023.08.28          RApiSerialize_0.1.2        
##  [43] jpeg_0.1-10                 ggraph_2.1.0               
##  [45] sctransform_0.4.1           sessioninfo_1.2.2          
##  [47] DBI_1.1.3                   jquerylib_0.1.4            
##  [49] withr_2.5.1                 systemfonts_1.0.4          
##  [51] class_7.3-22                rprojroot_2.0.3            
##  [53] lmtest_0.9-40               bdsmatrix_1.3-6            
##  [55] tidygraph_1.2.3             BiocManager_1.30.22        
##  [57] htmlwidgets_1.6.2           fs_1.6.3                   
##  [59] SingleCellExperiment_1.22.0 segmented_1.6-4            
##  [61] labeling_0.4.3              cellranger_1.1.0           
##  [63] MatrixGenerics_1.12.3       reticulate_1.38.0          
##  [65] zoo_1.8-12                  GGally_2.2.0               
##  [67] XVector_0.40.0              timechange_0.2.0           
##  [69] foreach_1.5.2               fansi_1.0.5                
##  [71] caTools_1.18.2              timeDate_4022.108          
##  [73] ggiraph_0.8.7               RSpectra_0.16-1            
##  [75] irlba_2.3.5.1               gridGraphics_0.5-1         
##  [77] ellipsis_0.3.2              lazyeval_0.2.2             
##  [79] yaml_2.3.7                  survival_3.5-5             
##  [81] scattermore_1.2             crayon_1.5.2               
##  [83] RcppAnnoy_0.0.21            progressr_0.14.0           
##  [85] tweenr_2.0.2                later_1.3.1                
##  [87] profvis_0.3.8               ggridges_0.5.4             
##  [89] codetools_0.2-19            base64enc_0.1-3            
##  [91] GlobalOptions_0.1.2         KEGGREST_1.40.1            
##  [93] bbmle_1.0.25                Rtsne_0.16                 
##  [95] shape_1.4.6                 filelock_1.0.2             
##  [97] foreign_0.8-84              pkgconfig_2.0.3            
##  [99] xml2_1.3.5                  mathjaxr_1.6-0             
## [101] EnvStats_2.8.1              GenomicRanges_1.52.1       
## [103] aplot_0.2.2                 spatstat.sparse_3.0-2      
## [105] ape_5.7-1                   viridisLite_0.4.2          
## [107] xtable_1.8-4                plyr_1.8.9                 
## [109] httr_1.4.7                  globals_0.16.2             
## [111] hardhat_1.3.0               pkgbuild_1.4.2             
## [113] beeswarm_0.4.0              htmlTable_2.4.2            
## [115] checkmate_2.3.0             nlme_3.1-162               
## [117] loo_2.6.0                   HDO.db_0.99.1              
## [119] dbplyr_2.3.4                lme4_1.1-35.1              
## [121] digest_0.6.33               Matrix_1.6-1.1             
## [123] farver_2.1.2                tzdb_0.4.0                 
## [125] reshape2_1.4.4              ModelMetrics_1.2.2.2       
## [127] yulab.utils_0.1.0           viridis_0.6.4              
## [129] rpart_4.1.19                glue_1.6.2                 
## [131] cachem_1.0.8                BiocFileCache_2.8.0        
## [133] polyclip_1.10-6             Hmisc_5.1-1                
## [135] generics_0.1.3              Biostrings_2.68.1          
## [137] classInt_0.4-10             CompQuadForm_1.4.3         
## [139] mvtnorm_1.2-3               parallelly_1.36.0          
## [141] pkgload_1.3.3               statmod_1.5.0              
## [143] minqa_1.2.6                 pbapply_1.7-2              
## [145] SummarizedExperiment_1.30.2 vroom_1.6.4                
## [147] gson_0.1.0                  utf8_1.2.3                 
## [149] gower_1.0.1                 graphlayouts_1.0.2         
## [151] StanHeaders_2.26.28         readxl_1.4.3               
## [153] gridExtra_2.3               shiny_1.7.5                
## [155] lava_1.7.3                  GenomeInfoDbData_1.2.10    
## [157] RCurl_1.98-1.12             memoise_2.0.1              
## [159] rmarkdown_2.25              pheatmap_1.0.12            
## [161] downloader_0.4              RANN_2.6.1                 
## [163] stringfish_0.15.8           spatstat.data_3.0-1        
## [165] rstudioapi_0.15.0           cluster_2.1.4              
## [167] QuickJSR_1.0.7              rstantools_2.3.1.1         
## [169] spatstat.utils_3.0-3        hms_1.1.3                  
## [171] fitdistrplus_1.1-11         munsell_0.5.0              
## [173] rlang_1.1.1                 GenomeInfoDb_1.36.4        
## [175] ipred_0.9-14                circlize_0.4.15            
## [177] mgcv_1.8-42                 xfun_0.48                  
## [179] e1071_1.7-13                metafor_4.6-0              
## [181] remotes_2.4.2.1             recipes_1.0.8              
## [183] iterators_1.0.14            matrixStats_1.0.0          
## [185] reldist_1.7-2               abind_1.4-5                
## [187] rstan_2.32.3                treeio_1.24.3              
## [189] rJava_1.0-6                 fftwtools_0.9-11           
## [191] bitops_1.0-7                ps_1.7.5                   
## [193] promises_1.2.1              inline_0.3.19              
## [195] scatterpie_0.2.1            RSQLite_2.3.1              
## [197] qvalue_2.32.0               proxy_0.4-27               
## [199] fgsea_1.26.0                DelayedArray_0.26.7        
## [201] GO.db_3.17.0                compiler_4.3.1             
## [203] RBioFormats_1.0.0           prettyunits_1.2.0          
## [205] listenv_0.9.0               tensor_1.5                 
## [207] units_0.8-5                 MASS_7.3-60                
## [209] progress_1.2.2              uuid_1.1-1                 
## [211] BiocParallel_1.34.2         gridtext_0.1.5             
## [213] EBImage_4.42.0              babelgene_22.9             
## [215] spatstat.random_3.1-6       R6_2.5.1                   
## [217] fastmap_1.1.1               fastmatch_1.1-4            
## [219] vipor_0.4.5                 ROCR_1.0-11                
## [221] ggstats_0.5.1               nnet_7.3-19                
## [223] gtable_0.3.4                KernSmooth_2.23-21         
## [225] miniUI_0.1.1.1              deldir_1.0-9               
## [227] ggthemes_5.0.0              htmltools_0.5.6.1          
## [229] RcppParallel_5.1.7          bit64_4.0.5                
## [231] spatstat.explore_3.2-3      lifecycle_1.0.3            
## [233] zip_2.3.0                   processx_3.8.2             
## [235] nloptr_2.0.3                callr_3.7.3                
## [237] xlsxjars_0.6.1              sass_0.4.7                 
## [239] vctrs_0.6.3                 spatstat.geom_3.2-5        
## [241] DOSE_3.26.2                 ggfun_0.1.3                
## [243] future.apply_1.11.0         entropy_1.3.1              
## [245] bslib_0.5.1                 pillar_1.9.0               
## [247] magick_2.8.2                gplots_3.1.3               
## [249] locfit_1.5-9.8              BiocStyle_2.28.1           
## [251] jsonlite_1.8.7              GetoptLong_1.0.5